9FS1

Mutant S1538L of the dihydroorotase domain of human CAD protein bound to carbamoyl aspartate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free: 0.151 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.131 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Disruption of CAD Oligomerization by Pathogenic Variants.

Del Cano-Ochoa, F.Ramadane-Morchadi, L.Eixeres, L.Moreno-Morcillo, M.Fernandez-Leiro, R.Ramon-Maiques, S.

(2024) J Mol Biol 436: 168832-168832

  • DOI: https://doi.org/10.1016/j.jmb.2024.168832
  • Primary Citation of Related Structures:  
    9FS1, 9FS2, 9FS3

  • PubMed Abstract: 

    CAD, the multi-enzymatic protein essential for initiating the de novo biosynthesis of pyrimidine nucleotides, forms large hexamers whose structure and function are not fully understood. Defects in CAD cause a severe neurometabolic disorder that is challenging to diagnose. We developed a cellular functional assay to identify defective CAD variants, and in this study, we characterized five pathogenic missense mutations in CAD's dihydroorotase (DHO) and aspartate transcarbamoylase (ATC) domains. All mutations impaired enzymatic activities, with two notably disrupting the formation of DHO dimers and ATC trimers. Combining crystal structures and AlphaFold predictions, we modeled the hexameric CAD complex, highlighting the central role of the DHO and ATC domains in its assembly. Our findings provide insight into CAD's stability, function, and organization, revealing that correct oligomerization of CAD into a supramolecular complex is required for its function in nucleotide synthesis and that mutations affecting this assembly are potentially pathogenic.


  • Organizational Affiliation

    Structure of Macromolecular Targets Unit, Instituto de Biomedicina de Valencia (IBV), CSIC, Eduardo Primo Yúfera, 3, 46012 Valencia, Spain. Electronic address: fdelcano@ibv.csic.es.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Multifunctional protein CAD362Homo sapiensMutation(s): 1 
Gene Names: CAD
EC: 6.3.5.5 (PDB Primary Data), 3.5.1.2 (PDB Primary Data), 6.3.4.16 (PDB Primary Data), 2.1.3.2 (PDB Primary Data), 3.5.2.3 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P27708 (Homo sapiens)
Explore P27708 
Go to UniProtKB:  P27708
PHAROS:  P27708
GTEx:  ENSG00000084774 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27708
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NCD
Query on NCD

Download Ideal Coordinates CCD File 
B [auth A]N-CARBAMOYL-L-ASPARTATE
C5 H8 N2 O5
HLKXYZVTANABHZ-REOHCLBHSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
F [auth A],
H [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
FMT
Query on FMT

Download Ideal Coordinates CCD File 
E [auth A],
G [auth A]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
A
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.331α = 90
b = 158.718β = 90
c = 61.947γ = 90
Software Package:
Software NamePurpose
EDNAdata collection
autoPROCdata processing
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministerio de Ciencia e Innovacion (MCIN)SpainPID2021-128468NB-I00
Other privateFundacion Ramon Areces

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-04
    Type: Initial release